
Extract Intan Data
--------------------
Creating empty HDF5 store with raw data groups
Writing RN18_ctaTrain.h5 ...Done!

Creating empty arrays in hdf5 store for raw data...Done!
Extracting Intan data to HDF5 Store:
 h5 file: /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5

Reading time data...
Writing time data...Done!

----------
Extracting Digital Signal Data
----------
Reading digitalin data from board-DIN-00.dat...Done!
Writing data from ditigal in channel 0 to dig_in_0...Done!
Done! Elapsed Time: 0.58


----------
Extracting Amplifier Signal Data
----------
Reading data from amp-C-000.dat...Done!
Writing data from port C channel 0 to electrode0...Done!
Reading data from amp-C-001.dat...Done!
Writing data from port C channel 1 to electrode1...Done!
Reading data from amp-C-002.dat...Done!
Writing data from port C channel 2 to electrode2...Done!
Reading data from amp-C-003.dat...Done!
Writing data from port C channel 3 to electrode3...Done!
Reading data from amp-C-004.dat...Done!
Writing data from port C channel 4 to electrode4...Done!
Reading data from amp-C-005.dat...Done!
Writing data from port C channel 5 to electrode5...Done!
Reading data from amp-C-006.dat...Done!
Writing data from port C channel 6 to electrode6...Done!
Reading data from amp-C-007.dat...Done!
Writing data from port C channel 7 to electrode7...Done!
Reading data from amp-C-008.dat...Done!
Writing data from port C channel 8 to electrode8...Done!
Reading data from amp-C-009.dat...Done!
Writing data from port C channel 9 to electrode9...Done!
Reading data from amp-C-010.dat...Done!
Writing data from port C channel 10 to electrode10...Done!
Reading data from amp-C-011.dat...Done!
Writing data from port C channel 11 to electrode11...Done!
Reading data from amp-C-012.dat...Done!
Writing data from port C channel 12 to electrode12...Done!
Reading data from amp-C-013.dat...Done!
Writing data from port C channel 13 to electrode13...Done!
Reading data from amp-C-014.dat...Done!
Writing data from port C channel 14 to electrode14...Done!
Reading data from amp-C-015.dat...Done!
Writing data from port C channel 15 to electrode15...Done!
Reading data from amp-C-016.dat...Done!
Writing data from port C channel 16 to electrode16...Done!
Reading data from amp-C-017.dat...Done!
Writing data from port C channel 17 to electrode17...Done!
Reading data from amp-C-018.dat...Done!
Writing data from port C channel 18 to electrode18...Done!
Reading data from amp-C-019.dat...Done!
Writing data from port C channel 19 to electrode19...Done!
Reading data from amp-C-020.dat...Done!
Writing data from port C channel 20 to electrode20...Done!
Reading data from amp-C-021.dat...Done!
Writing data from port C channel 21 to electrode21...Done!
Reading data from amp-C-022.dat...Done!
Writing data from port C channel 22 to electrode22...Done!
Reading data from amp-C-023.dat...Done!
Writing data from port C channel 23 to electrode23...Done!
Reading data from amp-C-024.dat...Done!
Writing data from port C channel 24 to electrode24...Done!
Reading data from amp-C-025.dat...Done!
Writing data from port C channel 25 to electrode25...Done!
Reading data from amp-C-026.dat...Done!
Writing data from port C channel 26 to electrode26...Done!
Reading data from amp-C-027.dat...Done!
Writing data from port C channel 27 to electrode27...Done!
Reading data from amp-C-028.dat...Done!
Writing data from port C channel 28 to electrode28...Done!
Reading data from amp-C-029.dat...Done!
Writing data from port C channel 29 to electrode29...Done!
Reading data from amp-C-030.dat...Done!
Writing data from port C channel 30 to electrode30...Done!
Reading data from amp-C-031.dat...Done!
Writing data from port C channel 31 to electrode31...Done!
Done! Elapsed Time: 18.20

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Writing digital_input_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p


Data Extraction Complete
--------------------

----------
Gathering Trial Data and Creating Table
----------
Generating trial list for digital inputs: 0
Grabbing data for digital input 0...Done!
Constructing DataFrame...Done!
Writing data to h5 file...Done!
Done! Elapsed Time: 0.31

No digital output data found
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

CAR Groups

Group 0	Group 1
-------	-------
0	8
1	9
2	10
3	11
4	12
5	13
6	14
7	15
24	16
25	17
26	18
27	19
28	20
29	21
30	22
31	23

----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29, 30, 31
Some raw voltage traces are different lengths.
This could be a sign that recording was cutoff early.
Truncating to the length of the shortest trace for analysis
    Min Samples: 29767680
    Max Samples: 29775872
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 15.55


----------
Common Average Referencing
----------
Common Average Referencing Electrodes:
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
Some raw voltage traces are different lengths.
This could be a sign that recording was cutoff early.
Truncating to the length of the shortest trace for analysis
    Min Samples: 29767680
    Max Samples: 29775872
Computing common average...Done!
Storing common average signal...Done!
Storing referenced signals...Done!
Done! Elapsed Time: 13.60


----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5 as /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5
Done! Elapsed Time: 88.66

Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p


Running Spike Detection
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      7
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Electrode    Result    Cutoff (s)
  0            1         992
  1            1         992
  2            1         992
  3            1         992
  4            1         992
  5            1         992
  6            1         992
  11           1         992
  12           1         992
  13           1         992
  14           1         992
  15           1         992
  16           1         992
  17           1         992
  18           1         992
  19           1         992
  20           1         992
  21           1         992
  22           1         992
  23           1         992
  24           1         992
  25           1         992
  26           1         992
  27           1         992
  28           1         992
  29           1         992
  30           1         992
  31           1         992
1 - Sucess
0 - No data or no spikes
-1 - Error
Writing electrode_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Spike Detection Complete
------------------

----------
Clustering Cleanup
----------
Removing raw data from hdf5 store...Done!
Removing referenced data from hdf5 store...Done!

----------
Compressing and repacking h5 file
----------
Repacking /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5 as /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/tmp.h5...
Removing old h5 file: /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5
Renaming temporary file to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5
Done! Elapsed Time: 8.10

Done! Elapsed Time: 11.18

Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p


Running Blech Clust
-------------------
Parameters
file_dir             /data/Katz_Data/Stk11_Project/RN18/RN18_4taste_preCTA_190921_134057
data_quality         clean
sampling_rate        30000.0
clustering_params    
    Max Number of Clusters      15
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params          
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params      
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot       
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Clustering Complete
------------------

Running Blech Clust
-------------------
Parameters
file_dir                  /data/Katz_Data/Stk11_Project/RN18/RN18_4taste_preCTA_190921_134057
data_quality              clean
sampling_rate             30000.0
clustering_params         
    Max Number of Clusters      15
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params               
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params           
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot            
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    
max_clusters              15
max_iterations            1000
threshold                 0.001
num_restarts              10
wf_amplitude_sd_cutoff    3

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Clustering Complete
------------------

Running Blech Clust
-------------------
Parameters
file_dir                  /data/Katz_Data/Stk11_Project/RN18/RN18_4taste_preCTA_190921_134057
data_quality              clean
sampling_rate             30000.0
clustering_params         
    Max Number of Clusters      15
    Max Number of Iterations    1000
    Convergence Criterion       0.001
    GMM random restarts         10
    
data_params               
    V_cutoff for disconnected headstage     1500
    Max rate of cutoff breach per second    0.2
    Max allowed seconds with a breach       10
    Max allowed breaches per second         20
    Intra-cluster waveform amp SD cutoff    3
    
bandpass_params           
    Lower freq cutoff    300
    Upper freq cutoff    3000
    
spike_snapshot            
    Time before spike (ms)    0.5
    Time after spike (ms)     1
    
max_clusters              15
max_iterations            1000
threshold                 0.001
num_restarts              10
wf_amplitude_sd_cutoff    3

Writing electrode_map to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain.h5...
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Clustering Complete
------------------

----------
Clustering Cleanup
----------
Done! Elapsed Time: 0.01

Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p


---------
Beginning unit similarity calculation
----------
Computing similarity between Unit 0 and Unit 0
Computing similarity between Unit 0 and Unit 1
Computing similarity between Unit 0 and Unit 2
Computing similarity between Unit 0 and Unit 3
Computing similarity between Unit 0 and Unit 4
Computing similarity between Unit 1 and Unit 0
Computing similarity between Unit 1 and Unit 1
Computing similarity between Unit 1 and Unit 2
Computing similarity between Unit 1 and Unit 3
Computing similarity between Unit 1 and Unit 4
Computing similarity between Unit 2 and Unit 0
Computing similarity between Unit 2 and Unit 1
Computing similarity between Unit 2 and Unit 2
Computing similarity between Unit 2 and Unit 3
Computing similarity between Unit 2 and Unit 4
Computing similarity between Unit 3 and Unit 0
Computing similarity between Unit 3 and Unit 1
Computing similarity between Unit 3 and Unit 2
Computing similarity between Unit 3 and Unit 3
Computing similarity between Unit 3 and Unit 4
Computing similarity between Unit 4 and Unit 0
Computing similarity between Unit 4 and Unit 1
Computing similarity between Unit 4 and Unit 2
Computing similarity between Unit 4 and Unit 3
Computing similarity between Unit 4 and Unit 4

Similarity calculation done!
No unit similarity violations found!
Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Generating unit arrays with parameters:
----------
    dig_ins_to_use    
            0
    laser_channels    
        
    sampling_rate     30000.0
    pre_stimulus      2000
    post_stimulus     5000
    

----------
Making Unit Spike Arrays
----------


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01


----------
Reading Trial Data Table From Store
----------
Done! Elapsed Time: 0.01

Creating spike arrays for dig_in_0...
Done with spike array creation!
----------

Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

Saved RN18_ctaTrain to /data/Katz_Data/Stk11_Project/RN18/RN18_ctaTrain_190922_123953/RN18_ctaTrain_dataset.p

